Merge pull request #151 from yucongalicechen/utils-update

fix: update functions related to `diffpy.utils` update

news/utils-updates.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Functions that use DiffractionObject` in `diffpy.utils` to follow the new API.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/labpdfproc/functions.py

@@ -5,11 +5,13 @@
 import pandas as pd
 from scipy.interpolate import interp1d
 
-from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object
+from diffpy.utils.diffraction_objects import XQUANTITIES, DiffractionObject
 
 RADIUS_MM = 1
 N_POINTS_ON_DIAMETER = 300
 TTH_GRID = np.arange(1, 180.1, 0.1)
+# Round down the last element if it's slightly above 180 due to floating point precision
+TTH_GRID[-1] = 180.00
 CVE_METHODS = ["brute_force", "polynomial_interpolation"]
 
 # pre-computed datasets for polynomial interpolation (fast calculation)
@@ -191,14 +193,14 @@ def _cve_brute_force(diffraction_data, mud):
     muls = np.array(muls) / abs_correction.total_points_in_grid
     cve = 1 / muls
 
-    cve_do = Diffraction_object(wavelength=diffraction_data.wavelength)
-    cve_do.insert_scattering_quantity(
-        TTH_GRID,
-        cve,
-        "tth",
-        metadata=diffraction_data.metadata,
-        name=f"absorption correction, cve, for {diffraction_data.name}",
+    cve_do = DiffractionObject(
+        xarray=TTH_GRID,
+        yarray=cve,
+        xtype="tth",
+        wavelength=diffraction_data.wavelength,
         scat_quantity="cve",
+        name=f"absorption correction, cve, for {diffraction_data.name}",
+        metadata=diffraction_data.metadata,
     )
     return cve_do
 
@@ -211,22 +213,22 @@ def _cve_polynomial_interpolation(diffraction_data, mud):
     if mud > 6 or mud < 0.5:
         raise ValueError(
             f"mu*D is out of the acceptable range (0.5 to 6) for polynomial interpolation. "
-            f"Please rerun with a value within this range or specifying another method from {* CVE_METHODS, }."
+            f"Please rerun with a value within this range or specifying another method from {*CVE_METHODS, }."
         )
     coeff_a, coeff_b, coeff_c, coeff_d, coeff_e = [
         interpolation_function(mud) for interpolation_function in INTERPOLATION_FUNCTIONS
     ]
     muls = np.array(coeff_a * MULS**4 + coeff_b * MULS**3 + coeff_c * MULS**2 + coeff_d * MULS + coeff_e)
     cve = 1 / muls
 
-    cve_do = Diffraction_object(wavelength=diffraction_data.wavelength)
-    cve_do.insert_scattering_quantity(
-        TTH_GRID,
-        cve,
-        "tth",
-        metadata=diffraction_data.metadata,
-        name=f"absorption correction, cve, for {diffraction_data.name}",
+    cve_do = DiffractionObject(
+        xarray=TTH_GRID,
+        yarray=cve,
+        xtype="tth",
+        wavelength=diffraction_data.wavelength,
         scat_quantity="cve",
+        name=f"absorption correction, cve, for {diffraction_data.name}",
+        metadata=diffraction_data.metadata,
     )
     return cve_do
 
@@ -257,7 +259,7 @@ def compute_cve(diffraction_data, mud, method="polynomial_interpolation", xtype=
     xtype str
       the quantity on the independent variable axis, allowed values are {*XQUANTITIES, }
     method str
-      the method used to calculate cve, must be one of {* CVE_METHODS, }
+      the method used to calculate cve, must be one of {*CVE_METHODS, }
 
     Returns
     -------
@@ -270,14 +272,14 @@ def compute_cve(diffraction_data, mud, method="polynomial_interpolation", xtype=
     global_xtype = cve_do_on_global_grid.on_xtype(xtype)[0]
     cve_on_global_xtype = cve_do_on_global_grid.on_xtype(xtype)[1]
     newcve = np.interp(orig_grid, global_xtype, cve_on_global_xtype)
-    cve_do = Diffraction_object(wavelength=diffraction_data.wavelength)
-    cve_do.insert_scattering_quantity(
-        orig_grid,
-        newcve,
-        xtype,
-        metadata=diffraction_data.metadata,
-        name=f"absorption correction, cve, for {diffraction_data.name}",
+    cve_do = DiffractionObject(
+        xarray=orig_grid,
+        yarray=newcve,
+        xtype=xtype,
+        wavelength=diffraction_data.wavelength,
         scat_quantity="cve",
+        name=f"absorption correction, cve, for {diffraction_data.name}",
+        metadata=diffraction_data.metadata,
     )
     return cve_do
 

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -5,8 +5,8 @@
 
 from diffpy.labpdfproc.functions import CVE_METHODS, apply_corr, compute_cve
 from diffpy.labpdfproc.tools import known_sources, load_metadata, preprocessing_args
+from diffpy.utils.diffraction_objects import XQUANTITIES, DiffractionObject
 from diffpy.utils.parsers.loaddata import loadData
-from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object
 
 
 def define_arguments():
@@ -170,12 +170,12 @@ def main():
                 f"exists. Please rerun specifying -f if you want to overwrite it."
             )
 
-        input_pattern = Diffraction_object(wavelength=args.wavelength)
         xarray, yarray = loadData(filepath, unpack=True)
-        input_pattern.insert_scattering_quantity(
-            xarray,
-            yarray,
-            args.xtype,
+        input_pattern = DiffractionObject(
+            xarray=xarray,
+            yarray=yarray,
+            xtype=args.xtype,
+            wavelength=args.wavelength,
             scat_quantity="x-ray",
             name=filepath.stem,
             metadata=load_metadata(args, filepath),

src/diffpy/labpdfproc/tools.py

@@ -1,11 +1,10 @@
 import copy
 from pathlib import Path
 
-from diffpy.labpdfproc.mud_calculator import compute_mud
-from diffpy.utils.scattering_objects.diffraction_objects import QQUANTITIES, XQUANTITIES
-from diffpy.utils.tools import get_package_info, get_user_info
+from diffpy.utils.diffraction_objects import ANGLEQUANTITIES, QQUANTITIES, XQUANTITIES
+from diffpy.utils.tools import check_and_build_global_config, compute_mud, get_package_info, get_user_info
 
-WAVELENGTHS = {"Mo": 0.71, "Ag": 0.59, "Cu": 1.54}
+WAVELENGTHS = {"Mo": 0.71073, "Ag": 0.59, "Cu": 1.5406}
 known_sources = [key for key in WAVELENGTHS.keys()]
 
 # Exclude wavelength from metadata to prevent duplication,
@@ -154,7 +153,9 @@ def set_xtype(args):
     """
     if args.xtype.lower() not in XQUANTITIES:
         raise ValueError(f"Unknown xtype: {args.xtype}. Allowed xtypes are {*XQUANTITIES, }.")
-    args.xtype = "q" if args.xtype.lower() in QQUANTITIES else "tth"
+    args.xtype = (
+        "q" if args.xtype.lower() in QQUANTITIES else "tth" if args.xtype.lower() in ANGLEQUANTITIES else "d"
+    )
     return args
 
 
@@ -224,7 +225,8 @@ def load_user_metadata(args):
 
 def load_user_info(args):
     """
-    Update username and email using get_user_info function from diffpy.utils
+    Load user info into args. If args are not provided, call check_and_build_global_config function from
+    diffpy.utils to prompt the user for inputs. Otherwise, call get_user_info with the provided arguments.
 
     Parameters
     ----------
@@ -236,10 +238,11 @@ def load_user_info(args):
     the updated argparse Namespace with username and email inserted
 
     """
-    config = {"username": args.username, "email": args.email}
-    config = get_user_info(config)
-    args.username = config["username"]
-    args.email = config["email"]
+    if args.username is None or args.email is None:
+        check_and_build_global_config()
+    config = get_user_info(owner_name=args.username, owner_email=args.email)
+    args.username = config.get("owner_name")
+    args.email = config.get("owner_email")
     return args
 
 

tests/conftest.py

@@ -49,7 +49,11 @@ def user_filesystem(tmp_path):
         f.write("good_data.xy \n")
         f.write(f"{str(input_dir.resolve() / 'good_data.txt')}\n")
 
-    home_config_data = {"username": "home_username", "email": "[email protected]"}
+    home_config_data = {
+        "owner_name": "home_username",
+        "owner_email": "[email protected]",
+        "owner_orcid": "home_orcid",
+    }
     with open(home_dir / "diffpyconfig.json", "w") as f:
         json.dump(home_config_data, f)
 

tests/test_fixtures.py

@@ -2,7 +2,7 @@
 
 import pytest
 
-from diffpy.utils.parsers import loadData
+from diffpy.utils.parsers.loaddata import loadData
 
 
 # Test that our readable and unreadable files are indeed readable and

tests/test_functions.py

@@ -4,7 +4,7 @@
 import pytest
 
 from diffpy.labpdfproc.functions import CVE_METHODS, Gridded_circle, apply_corr, compute_cve
-from diffpy.utils.scattering_objects.diffraction_objects import Diffraction_object
+from diffpy.utils.diffraction_objects import DiffractionObject
 
 params1 = [
     ([0.5, 3, 1], {(0.0, -0.5), (0.0, 0.0), (0.5, 0.0), (-0.5, 0.0), (0.0, 0.5)}),
@@ -59,11 +59,11 @@ def test_set_muls_at_angle(inputs, expected):
 
 
 def _instantiate_test_do(xarray, yarray, xtype="tth", name="test", scat_quantity="x-ray"):
-    test_do = Diffraction_object(wavelength=1.54)
-    test_do.insert_scattering_quantity(
-        xarray,
-        yarray,
-        xtype,
+    test_do = DiffractionObject(
+        xarray=xarray,
+        yarray=yarray,
+        xtype=xtype,
+        wavelength=1.54,
         scat_quantity=scat_quantity,
         name=name,
         metadata={"thing1": 1, "thing2": "thing2"},
@@ -81,14 +81,13 @@ def _instantiate_test_do(xarray, yarray, xtype="tth", name="test", scat_quantity
 def test_compute_cve(inputs, expected, mocker):
     xarray, yarray = np.array([90, 90.1, 90.2]), np.array([2, 2, 2])
     expected_cve = np.array([0.5, 0.5, 0.5])
-    mocker.patch("diffpy.labpdfproc.functions.TTH_GRID", xarray)
     mocker.patch("numpy.interp", return_value=expected_cve)
     input_pattern = _instantiate_test_do(xarray, yarray)
     actual_cve_do = compute_cve(input_pattern, mud=1, method="polynomial_interpolation", xtype=inputs[0])
     expected_cve_do = _instantiate_test_do(
-        expected[0],
-        expected[1],
-        expected[2],
+        xarray=expected[0],
+        yarray=expected[1],
+        xtype=expected[2],
         name="absorption correction, cve, for test",
         scat_quantity="cve",
     )
@@ -126,8 +125,8 @@ def test_apply_corr(mocker):
     mocker.patch("numpy.interp", return_value=expected_cve)
     input_pattern = _instantiate_test_do(xarray, yarray)
     absorption_correction = _instantiate_test_do(
-        xarray,
-        expected_cve,
+        xarray=xarray,
+        yarray=expected_cve,
         name="absorption correction, cve, for test",
         scat_quantity="cve",
     )